Research article
Defining the healthy "core microbiome" of oral microbial communities
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* Corresponding author: Egija Zaura e.zaura@acta.nl
1 Department of Cariology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Free University Amsterdam, the Netherlands
2 TNO Quality of Life, Business Unit Food and Biotechnology Innovations, Microbial Genomics Group, Zeist, the Netherlands
3 Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
BMC Microbiology 2009, 9:259 doi:10.1186/1471-2180-9-259
Published: 15 December 2009Additional files
Additional file 1:
Full list and taxonomy of OTUs clustered at 3% difference in descending order of their relative abundance (%). This is an Excel file listing all 818 OTUs, number of unique sequences within each OTU, abundance and the taxonomic assignment of each OTU per individual S1, S2 and S3.
Format: XLS Size: 149KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 2:
Full list and taxonomy of OTUs clustered at 6% difference in descending order of their relative abundance (%). This is an Excel file listing all 517 OTUs, abundance and the taxonomic assignment of each OTU per individual S1, S2 and S3.
Format: XLS Size: 116KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 3:
Full list and taxonomy of OTUs clustered at 10% difference in descending order of their relative abundance (%). This is an Excel file listing all 320 OTUs, abundance and the taxonomic assignment of each OTU per individual S1, S2 and S3.
Format: XLS Size: 95KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 4:
Full list and relative abundance of higher taxa per individual microbiome. This is an Excel file listing all 112 higher taxa (genera or more inclusive taxa when sequences could not be confidently classified to the genus level) and their relative abundance in oral microbiomes of three individuals: S1, S2 and S3.
Format: XLS Size: 42KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 5:
Relative abundance of 1660 unique sequences that were shared by three individuals (S1, S2 and S3). This Excel file lists the taxonomy of the sequences shared by three individuals, ranked by the abundance of these sequences in the total data set. The sequences are available at the Short Read Archive of NCBI as SRP000913.
Format: XLS Size: 3.2MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 6:
Full list and absolute abundance of higher taxa per individual sampling site. This is an Excel file listing all 112 higher taxa (genera or more inclusive taxa when sequences could not be confidently classified to the genus level) and their abundance in 29 samples from three individuals: S1, S2 and S3. Data were not normalized.
Format: XLS Size: 55KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 7:
Full list of taxa and PCA loadings. This is an Excel file listing the loadings of the first three components of the Principal Component Analysis (PCA) on all 818 OTUs (3% genetic difference) and all 29 samples (the corresponding PCA plots are shown in Figure 7). The loadings marked in bold and highlighted are above the arbitrary significance threshold of 1 or -1. The positive values are highlighted yellow; the negative values are highlighted turquoise.
Format: XLS Size: 128KB Download file
This file can be viewed with: Microsoft Excel Viewer